Genomic insight into a novel actinobacterium, Actinomadura rubrisoli sp. nov., reveals high potential for bioactive metabolites

Ay H.

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology, vol.114, no.2, pp.195-208, 2021 (SCI-Expanded) identifier identifier identifier

  • Publication Type: Article / Article
  • Volume: 114 Issue: 2
  • Publication Date: 2021
  • Doi Number: 10.1007/s10482-020-01511-5
  • Journal Name: Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology
  • Journal Indexes: Science Citation Index Expanded (SCI-EXPANDED), Scopus, Aquatic Science & Fisheries Abstracts (ASFA), BIOSIS, Biotechnology Research Abstracts, CAB Abstracts, EMBASE, Environment Index, Food Science & Technology Abstracts, MEDLINE, Veterinary Science Database
  • Page Numbers: pp.195-208
  • Keywords: Actinobacteria, Antimicrobial resistance genes, Biosynthetic gene clusters, Phylogenomics
  • Yıldız Technical University Affiliated: No


Isolation of novel actinobacteria from unexplored habitats as potential sources of novel drug leads has utmost importance. During the course of screening arid soil samples for novel actinobacteria, strain H3C3T was isolated from Malatya, Turkey and its taxonomic position was revealed by a genome-based polyphasic approach. Pairwise sequence comparison of the 16S rRNA gene showed that the strain is closely related to Actinomadura fibrosa JCM 9371T with sequence identity level of 99.0%. Comparative genome analyses based on digital DNA-DNA hybridization and average nucleotide identity indicated that strain H3C3T represents a novel species within the genus Actinomadura. The strain has typical characteristics of the genus Actinomadura, i.e. meso-diaminopimelic acid as diagnostic amino acid; galactose, glucose, madurose and ribose as whole-cell sugars. Major menaquinones detected were MK-9(H6), MK-9(H8) and polar lipids were diphosphatidylglycerol, phosphatidylinositol, glycophospholipid and unknown phospholipid and lipids. Its genome size is approximately 10.2 Mb with G+C content of 71.6%. Further genomic analyses of strain H3C3T indicated its high potential for novel biosynthetic gene clusters coding for various chemical structures. On the basis of phenotypic and phylogenetic analyses, strain H3C3T represents a novel species of the genus Actinomadura, for which Actinomadura rubrisoli sp. nov. is proposed, and it holds high promise for novel biosynthetic metabolites of value to biopharmaceutical industry.